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    41 repositories

    • parsnp

      Public
      Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surroundin…
      C++
      •
      Other
      •27•145•31•0•Updated Oct 2, 2025Oct 2, 2025

    • TTT

      Public
      Python
      •0•2•0•0•Updated Sep 30, 2025Sep 30, 2025

    • verkko

      Public
      Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
      Python
      •33•364•20•0•Updated Sep 29, 2025Sep 29, 2025

    • HG002

      Public
      A complete diploid human genome
      5•134•1•0•Updated Sep 26, 2025Sep 26, 2025

    • T2T-Browser

      Public
      Genome browser hub for the T2T genomes and resources
      HTML
      •3•23•0•0•Updated Sep 26, 2025Sep 26, 2025

    • Mash

      Public
      Fast genome and metagenome distance estimation using MinHash
      C++
      •
      Other
      •94•420•83•3•Updated Sep 19, 2025Sep 19, 2025

    • HG002-issues

      Public
      HG002 human reference genome issue tracking and polishing
      0•11•30•0•Updated Sep 11, 2025Sep 11, 2025

    • GQC

      Public
      Python package for comparing genome assemblies and read data to the diploid Q100 benchmark
      Python
      •
      Other
      •0•12•1•0•Updated Sep 11, 2025Sep 11, 2025

    • canu

      Public
      A single molecule sequence assembler for genomes large and small.
      C++
      •179•693•5•2•Updated Sep 4, 2025Sep 4, 2025

    • ModDotPlot

      Public
      Python
      •
      MIT License
      •12•165•4•0•Updated Aug 29, 2025Aug 29, 2025

    • MetaCompass

      Public
      MetaCompass: Reference-guided Assembly of Metagenomes
      Python
      •
      Other
      •11•38•12•0•Updated Aug 13, 2025Aug 13, 2025

    • CHM13

      Public
      The complete sequence of a human genome
      Other
      •100•990•26•0•Updated Jul 14, 2025Jul 14, 2025

    • meryl

      Public
      A genomic k-mer counter (and sequence utility) with nice features.
      C
      •14•144•36•0•Updated Jul 4, 2025Jul 4, 2025

    • meryl-utility

      Public
      A collection of miscellaneous code used by Meryl, Canu and others.
      C
      •3•1•0•0•Updated Jul 4, 2025Jul 4, 2025

    • Primates

      Public
      Complete assemblies of non-human primate genomes
      Other
      •4•51•1•0•Updated May 20, 2025May 20, 2025

    • training

      Public
      Genome Assembly 102
      Shell
      •2•14•0•0•Updated Apr 23, 2025Apr 23, 2025

    • anianns

      Public
      ANI based satellite annotation
      Python
      •0•10•1•0•Updated Apr 17, 2025Apr 17, 2025

    • seqrequester

      Public
      A tool for summarizing, extracting, generating and modifying DNA sequences.
      C
      •4•23•2•0•Updated Dec 17, 2024Dec 17, 2024

    • harvest-tools

      Public
      C++
      •
      Other
      •6•10•15•0•Updated Dec 16, 2024Dec 16, 2024

    • Winnowmap

      Public
      Long read / genome alignment software
      nanoporepacbiogenome-analysis
      C
      •
      Other
      •29•302•32•1•Updated Nov 5, 2024Nov 5, 2024

    • MashMap

      Public
      A fast approximate aligner for long DNA sequences
      C++
      •
      Other
      •39•283•23•0•Updated Oct 11, 2024Oct 11, 2024

    • MetaCarvel

      Public
      MetaCarvel: A scaffolder for metagenomes
      genome-assemblyscaffoldermetagenomes
      C++
      •
      MIT License
      •17•14•3•3•Updated Sep 17, 2024Sep 17, 2024

    • merqury

      Public
      k-mer based assembly evaluation
      Shell
      •
      Other
      •21•327•38•0•Updated Jun 28, 2024Jun 28, 2024

    • SALSA

      Public
      SALSA: A tool to scaffold long read assemblies with Hi-C data
      long-readhicassemblyscaffold
      Python
      •
      MIT License
      •48•187•23•2•Updated May 17, 2024May 17, 2024

    • rukki

      Public
      Extracting paths from assembly graphs
      Rust
      •0•24•18•0•Updated Apr 26, 2024Apr 26, 2024

    • canu-regression

      Public
      Regression test cases and results for Canu.
      Shell
      •0•0•0•0•Updated Apr 5, 2024Apr 5, 2024

    • verkko-regression

      Public
      Test suite for Verkko.
      Perl
      •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • CHM13-issues

      Public
      CHM13 human reference genome issue tracking
      HTML
      •
      Other
      •3•20•0•0•Updated Jan 18, 2024Jan 18, 2024

    • MetagenomeScope

      Public
      Visualization tool for (meta)genome assembly graphs
      bioinformaticsmetagenomicsgenome-assemblyvisualization
      JavaScript
      •
      GNU General Public License v3.0
      •8•23•124•1•Updated Jan 3, 2024Jan 3, 2024

    • gingr

      Public
      C++
      •
      Other
      •5•14•15•1•Updated Dec 5, 2023Dec 5, 2023